| Seonghan Kim | 5 Articles |
Objectives
In this study, we performed comparative genomic and transcriptomic analysis of clinical isolates of Mycobacterium tuberculosis collected from patients with drug-susceptible tuberculosis (DS-TB). The clinical isolates were categorized based on treatment duration: standard 6 months or >6 months. Methods Study participants were recruited from a 2016 to 2018 tuberculosis cohort, and clinical M. tuberculosis isolates were collected from the sputum of patients with tuberculosis. We analyzed the genome and transcriptome of the isolated M. tuberculosis. Results Genomic analysis revealed a specific non-synonymous single-nucleotide polymorphism in pe_pgrs9 and ppe34, exclusive to the group treated for >6 months. Transcriptomic analysis revealed increased expression of various virulence-associated protein family genes and decreased expression of ribosomal protein genes and ppe38 genes in the group treated for >6 months. Conclusion The identified genetic variation and gene expression patterns may influence treatment outcomes by modulating host immune responses, increasing virulence, and potentially contributing to persister cell formation in M. tuberculosis. This study provides insights into the genetic and transcriptomic factors associated with prolonged DS-TB treatment. However, our study identified molecular characteristics using a small sample size, and further detailed studies are warranted. Citations
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Objectives
<i>Mycobacterium intracellulare</i> is the major causative agent of nontuberculous mycobacteria-related pulmonary infections. The strain typing of <i>M. intracellulare</i> is important for the treatment and control of its infections. We compared the discrimination capacity and effective value of four different molecular typing methods. Methods Antibiotic susceptibility testing, <i>hsp65</i> and <i>rpoB</i> sequencing, pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), mycobacteria interspersed repetitive-unit-variable-number tandem-repeat analysis (MIRU-VNTR), and VNTR assay targeting 44 <i>M. intracellulare</i> isolates obtained from patients with pulmonary infections were performed. Results All the antibiotic susceptibility patterns had no association with the molecular and sequence types tested in this study; however, the molecular and sequence types were related with each other. PFGE gave best results for discriminatory capacity, followed by VNTR, MLST, and MIRU-VNTR. Conclusion The high discriminatory power of PFGE, VNTR, and MLST is enough for differentiating between reinfection and relapse, as well as for other molecular epidemiological usages. The MLST could be regarded as a representative classification method, because it showed the clearest relation with the sequence types. Citations
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Objectives
A multiplex real-time polymerase chain reaction (RT-PCR) method was developed for the identification of three <i>Vibrio</i> species: <i>Vibrio cholerae</i>, <i>Vibrio parahaemolyticus</i>, and <i>Vibrio vulnificus</i>. Methods Specific primers and probes targeting the <i>hlyA</i>, <i>tlh</i>, and <i>vvhA</i> genes were selected and used for multiplex real-time PCR to confirm the identification of <i>V. cholerae</i>, <i>V. parahaemolyticus</i>, and <i>V. vulnificus</i>, respectively. This method was applied to screen <i>Vibrio</i> species from environmental samples and combining it with a culture-based method, its effectiveness was evaluated in comparison with culture-based methods alone. Results Specific PCR fragments were obtained from isolates belonging to the target species, indicating a high specificity of this multiplex real-time PCR. No cross-reactivity with the assay was observed between the tested bacteria. The sensitivity of the multiplex real-time PCR was found to have a lower limit of 10<sup>4</sup> colony-forming units/reaction for all three <i>Vibrio</i> species. The combination strategy raised the isolation ratio of all three <i>Vibrio</i> species 1.26- to 2.75-fold. Conclusion This assay provides a rapid, sensitive, and specific technique to detect these three <i>Vibrio</i> species in the environment. Citations
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Objective
In this study, the factors that induced a decrease in the incidence of typhoid fever were analyzed. Based on the study results, we propose a quantitative and concrete solution to reduce the incidence of typhoid fever. Methods We analyzed the incidence and fatality rate of typhoid fever in Korea. Tap water service rate and the number of pharmacies, which affect the incidence rate of typhoid fever, were used as environmental factors. Results To prevent typhoid fever in the community, it is necessary to provide clean tap water service to 35.5% of the population, with an individual requiring 173 L of clean water daily. Appropriate access to clean water (51% service coverage, 307 L) helped the population to maintain individual hygiene and food safety practices, which brought about a decrease in the incidence of typhoid fever, and subsequently a decrease in fatality rate, which was achieved twice. During the 8-year study period, the fatality rate decreased to 1% when the population has access to proper medical service. Conclusion The fatality rate was primarily affected by the availability of medical services as well as by the incidence of typhoid fever. However, an analysis of the study results showed that the incidence of typhoid fever was affected only by the availability of clean water through the tap water system. Citations
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Two real-time polymerase chain reaction assays were developed to detect mutations in codons 83 and 87 in <i>gyrA</i> and in codons 80 and 91 in <i>parC</i>, the main sites that causes quinolone resistance in pathogenic <i>Escherichia coli </i>and <i>Shigella</i> spp. isolates. These assays can be employed as a useful method for controlling infections caused by quinolone-resistant <i>E coli </i>and <i>Shigella</i> isolates.
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